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3q61

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==3'-Fluoro Hexitol Nucleic Acid DNA Structure==
==3'-Fluoro Hexitol Nucleic Acid DNA Structure==
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<StructureSection load='3q61' size='340' side='right' caption='[[3q61]], [[Resolution|resolution]] 1.56&Aring;' scene=''>
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<StructureSection load='3q61' size='340' side='right'caption='[[3q61]], [[Resolution|resolution]] 1.56&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3q61]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3Q61 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3Q61 FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3q61]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3Q61 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3Q61 FirstGlance]. <br>
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</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=F3H:1,5-ANHYDRO-2,3-DIDEOXY-3-FLUORO-2-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)-6-O-PHOSPHONO-D-ALTRITOL'>F3H</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.56&#8491;</td></tr>
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<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3q61 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3q61 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3q61 RCSB], [http://www.ebi.ac.uk/pdbsum/3q61 PDBsum]</span></td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=F3H:1,5-ANHYDRO-2,3-DIDEOXY-3-FLUORO-2-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)-6-O-PHOSPHONO-D-ALTRITOL'>F3H</scene></td></tr>
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<table>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3q61 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3q61 OCA], [https://pdbe.org/3q61 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3q61 RCSB], [https://www.ebi.ac.uk/pdbsum/3q61 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3q61 ProSAT]</span></td></tr>
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<div style="background-color:#fffaf0;">
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</table>
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== Publication Abstract from PubMed ==
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The synthesis, biophysical, structural, and biological properties of both isomers of 3'-fluoro hexitol nucleic acid (FHNA and Ara-FHNA) modified oligonucleotides are reported. Synthesis of the FHNA and Ara-FHNA thymine phosphoramidites was efficiently accomplished starting from known sugar precursors. Optimal RNA affinities were observed with a 3'-fluorine atom and nucleobase in a trans-diaxial orientation. The Ara-FHNA analog with an equatorial fluorine was found to be destabilizing. However, the magnitude of destabilization was sequence-dependent. Thus, the loss of stability is sharply reduced when Ara-FHNA residues were inserted at pyrimidine-purine (Py-Pu) steps compared to placement within a stretch of pyrimidines (Py-Py). Crystal structures of A-type DNA duplexes modified with either monomer provide a rationalization for the opposing stability effects and point to a steric origin of the destabilization caused by the Ara-FHNA analog. The sequence dependent effect can be explained by the formation of an internucleotide C-F...H-C pseudo hydrogen bond between F3' of Ara-FHNA and C8-H of the nucleobase from the 3'-adjacent adenosine that is absent at Py-Py steps. In animal experiments, FHNA-modified antisense oligonucleotides formulated in saline showed a potent downregulation of gene expression in liver tissue without producing hepatotoxicity. Our data establish FHNA as a useful modification for antisense therapeutics and also confirm the stabilizing influence of F(Py)...H-C(Pu) pseudo hydrogen bonds in nucleic acid structures.
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Synthesis, improved antisense activity and structural rationale for the divergent RNA affinities of 3'-fluoro hexitol nucleic acid (FHNA and Ara-FHNA) modified oligonucleotides.,Egli M, Pallan PS, Allerson CR, Prakash TP, Berdeja A, Yu J, Lee S, Watt A, Gaus H, Bhat B, Swayze EE, Seth PP J Am Chem Soc. 2011 Oct 19;133(41):16642-9. Epub 2011 Sep 22. PMID:21919455<ref>PMID:21919455</ref>
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From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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</div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Allerson, C R.]]
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[[Category: Large Structures]]
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[[Category: Berdeja, A.]]
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[[Category: Allerson CR]]
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[[Category: Bhat, B.]]
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[[Category: Berdeja A]]
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[[Category: Egli, M.]]
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[[Category: Bhat B]]
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[[Category: Gaus, H.]]
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[[Category: Egli M]]
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[[Category: Pallan, P S.]]
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[[Category: Gaus H]]
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[[Category: Prakash, T P.]]
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[[Category: Pallan PS]]
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[[Category: Seth, P R.]]
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[[Category: Prakash TP]]
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[[Category: Siwkowski, A.]]
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[[Category: Seth PR]]
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[[Category: Swayze, E E.]]
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[[Category: Siwkowski A]]
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[[Category: Watt, A T.]]
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[[Category: Swayze EE]]
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[[Category: Yu, J.]]
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[[Category: Watt AT]]
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[[Category: 3'-fluoro hexitol nucleic acid]]
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[[Category: Yu J]]
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[[Category: A-form dna]]
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[[Category: Antisense oligonucleotide]]
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[[Category: Dna]]
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[[Category: Fhna]]
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Current revision

3'-Fluoro Hexitol Nucleic Acid DNA Structure

PDB ID 3q61

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